Installation

LMAS can be installed through Github (https://github.com/cimendes/LMAS). It requires a Nextflow installation (version ≥ 21.04.1) and can be used on any POSIX compatible system (Linux, OS X, etc). All components of LMAS are executed in `Docker containers<https://www.docker.com/>`_, being a container engine required.

Nextflow allows integration with multiple alternatives, such as Shifter or Singularity, so a particular one isn’t required.

To ensure the robustness of custom python code for the quality assessment of assemblies, continuous integration of the python templates is performed with pytest and GitHub Actions.

Below it’s a step by step guide on how to install LMAS and all its dependencies.

Step 1. Nextflow

Nextflow (version 20.01.0 or higher) can be used on any POSIX compatible system (Linux, OS X, etc). It requires BASH and Java 8 (or higher) to be installed.

Important

Instructions on how to install Nextflow are available here

Step 2. Container engine

All components of LMAS are executed in docker containers, which means that you’ll need to have a container engine installed. The container engines available are the ones supported by Nextflow:

If you already have any one of these installed, you are good to go as the provided docker containers are compatible with all engines available. If not, you’ll need to install one.

Singularity

Singularity is available to download and install here. Make sure that you have singularity v2.5.x or higher. Note that singularity should be installed as root and available on the machine(s) that will be running the nextflow processes.

Important

Singularity is available as a bioconda package. However, conda installs singularity in user space without root privileges, which may prevent singularity images from being correctly downloaded. Therefore it is not recommended that you install singularity via bioconda.

Docker

Docker can be installed following the instructions on the website: https://www.docker.com/community-edition#/download. To run docker as a non-root user, you’ll need to follow the instructions on the website: https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user

Step 3. Clone LMAS

You can clone this repository with git.

git clone https://github.com/cimendes/LMAS.git

All files will be on your local machine. The main execution file for Nextflow is LMAS.nf.